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{| align="center" width="100%" style="background: #B22222; margin-bottom: 4em; border-bottom: 1px solid #B22222; border-left: 1px solid #B22222; border-right: 1px solid #B22222;"
|+ style="width: 90%; font-size:190%; font-weight: bold; color:#038; text-align:center; padding: 5px; margin-bottom: 15px" | Welcome to the PyMOL Wiki
|+ style="font-size: 1.0em; font-weight: normal; color: #FFFFFF; text-align:right; background: #B22222; padding-top:0.5em; padding-bottom: 0.25em; padding-right: 0.60em; border-top: 2px solid #B22222; border-bottom: 1px solid #fff;" |hosted by [[File:SBGridlogo2.jpg|140 px|link=https://sbgrid.org/]]
|- style="text-align:center; font-weight:bold; color: #333; font-size: 120%"
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| We are the community-based support site for the popular molecular visualization program, [http://pymol.sf.net PyMOL].
{| align="center" style="padding-bottom: 3em;"
|-
|+ style="font-size:210%; font-weight: bold; color:#000000; text-align:center; padding: 5px; margin-bottom: 4px;" | Welcome to the PyMOL Wiki!
|- style="text-align:center; font-weight: normal; color: #000000; font-size: 120%; font-family: sans-serif;"
| The community-run support site for the [http://pymol.org PyMOL] molecular viewer.
|- style="text-align:center; font-weight:normal; color: #000000; font-size: 120%; font-family: sans-serif;"
| To request a new account, email SBGrid at:  accounts (@) sbgrid dot org
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{| align="center" width="45%" style="background: #FFFFFF; margin-bottom: 4em; border-bottom: 1px solid #AFB29E; border-left: 1px solid #AFB29E; border-right: 1px solid #AFB29E;"
{| align="center" style="width:90%; margin-bottom: 20px"
|+ style="font-size: 1.4em; font-weight: bold; color: #FFFFFF; text-align:center; background: #000000; padding-top:0.5em; padding-bottom: 0.25em; border-top: 2px solid #000000; border-bottom: 1px solid #fff;" |Quick Links
|
|-
{| align="left" width="20%" style="border: 1px solid #333; text-align:center; height=100%;"
| style="font-size: 1.1em; font-weight: normal; color #48A2B4; padding: 0.5em 1em 0.5em 3em;"|'''[[:Category:Tutorials|Tutorials]]''' || '''[[TOPTOC|Table of Contents]]''' || '''[[:Category:Commands|Commands]]'''
! style="font-weight: bold; font-size:120%; color: #333; background:#80AFFF;" | New Users
|-
|-
| style="background:#E6EFFF; color:#333; font-size: 110%; padding: 4.5px"| New users are encouraged to join. Feel free to add any appropriate content; make an account and get started!
| style="font-size: 1.1em; font-weight: normal; color #48A2B4; padding: 0.5em 1em 0.5em 3em;"|'''[[:Category:Script_Library|Script Library]]''' || '''[[:Category:Plugins|Plugins]]''' || '''[[:Category:FAQ|FAQ]]'''
|-
|-
| style="font-size: 1.1em; font-weight: normal; color #48A2B4; padding: 0.5em 1em 0.5em 3em;"|'''[[Gallery]]''' | '''[[Covers]]'''
||'''[[CheatSheet|PyMOL Cheat Sheet]]''' (''[[Media:PymolRef.pdf|PDF]]'')
||'''[[PyMOL_mailing_list|Getting Help]]'''
|}
|}
{| align="right" width="75%" style="border: 1px solid #333; text-align:left;"
 
! colspan="3" style="font-weight: bold; font-size:120%; color: #333; background:#80AFFF; text-align:center" | Quick Links
{| width="100%"
|-
| style="vertical-align: top; width: 40%" |
| [[TOPTOC|'''Table of Contents''']]
{| class="jtable" style="float: left; width: 90%;"
|| [[Special:Allpages|Index of all pages]]
|+ style="font-size: 1.4em; font-weight: bold; text-align:left; border-bottom: 2px solid #6678b1;" | News & Updates
|| [http://pymol.sf.net PyMOL] Homepage
|-
|-
| [[Practical_Pymol_for_Beginners|Beginner's Tutorial]]
! Official Release
|| [[:Category:Commands|PyMol Commands]]
| [https://pymol.org PyMOL v3.0 has been released] on March 12, 2024.
|| '''Settings''': [[Settings|All]] [[:Category:Settings|Documented]]
|-
|-
| [[:Category:Script_Library|'''Script Library''']]
! New Plugin
|| [[:Category:Plugins|'''Plugins''']]
| [[CavitOmiX|CavitOmiX]] calculate [https://innophore.com Catalophore™ cavities], predict protein structures with [https://www.nvidia.com/en-us/gpu-cloud/bionemo OpenFold by NVIDIA-BioNeMo], [https://ai.facebook.com/blog/protein-folding-esmfold-metagenomics/ ESMFold] and retrieve [https://www.deepmind.com/research/highlighted-research/alphafold Alphafold] models
|| [[:Special:Categories| See All Categories]]
|-
|-
| [[:Category:FAQ|Frequently Asked Questions]]
! Official Release
|| [[PyMolWiki:Community_Portal|'''How to get involved!''']]
| [https://pymol.org PyMOL v2.5 has been released] on May 10, 2021.
|| [[About| '''About PyMOL''']]
|-
|-
|}
! Python 3
|
| New [[2to3|Python 3 compatibility guide]] for scripts and plugins
|}
 
{| align="center" width="90%" style="background: #fafafa; border-right: 1px solid #333; border-left: 1px solid #333; border-bottom: 1px solid #333"
|+ style="text-align: left; font-weight:bold; font-size:150%; color:#333; background: #EFE6FF; padding:10px; border: 1px solid #333" | News and Updates ([[Older_News|archive]])
! style="font-weight: bold; font-size: 110%; text-decoration: underline; color: #000; padding: 12px; text-align: left;" | Wiki
|-
|-
| style="padding: 3px 5px 10px 15px;"| ♦ Updated the wiki.  Also installed the newer GeSHI extension.  Please keep an eye out for source code that is improperly tagged and so improperly formatted.  See [http://www.mediawiki.org/wiki/Extension:SyntaxHighlight_GeSHi#Parameters GeSHI Parameters].
! POSF
| [https://pymol.org/fellowship New PyMOL fellowship announced for 2022-2023]
|-
|-
| style="padding: 3px 5px 10px 15px;"| ♦ Adding a special category/section for active PyMOL [[:Category:Development|Development]].
! Tutorial
| [[Plugins Tutorial]] updated for PyQt5
|-
|-
|
! New Plugin
{|style="background-color: transparent;" width="100%"
| [[PICv|PICv]] is a new plugin for clustering protein-protein interactions and visualization with available data from PDBe
|-
|-
|valign="top"|
! Selection keywords
{|style="background-color: transparent;" width="100%"
| New [[Selection Algebra|polymer.protein and polymer.nucleic]] selection keywords. Thanks everyone who participated in the [https://goo.gl/forms/r0Ck03VTytZQxN4A2 poll]!
|-
|-
! style="font-weight: bold; font-size: 110%; text-decoration: underline; color: #000; padding: 12px; text-align: left;" | PyMOL
! Plugin Update
| [[MOLE 2.0: advanced approach for analysis of biomacromolecular channels|MOLE 2.5]] is an updated version of channel analysis software in PyMOL
|-
|-
| style="padding: 3px 5px 10px 15px;"| ♦ The truly awesome [[grid_mode]] setting has been added.
! New Script
| [[dssr_block]] is a wrapper for DSSR (3dna) and creates block-shaped nucleic acid cartoons
|-
|-
| style="padding: 3px 5px 10px 15px;"| ♦ [[Ellipsoids]] representation added for drawing thermal ellipsoids.
! Older News
|-
| See [[Older_News|Older News]].
| style="padding: 3px 5px 10px 15px;"| ♦ PyMOL 1.0 has been released!
|}
|style="vertical-align: top; width: 40%"|
{| class="jtable" style="float: right; width: 90%"
|+ style="font-size: 1.4em; font-weight: bold; text-align:left; border-bottom: 2px solid #6678b1;" |Did you know...
|-
|-
| style="padding: 3px 5px 10px 15px;"| ♦ [http://delsci.info/dsc/ PyMOL Official Documentation] is also available for subscribers.
|<div class="didyouknow" >
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|valign="bottom" width="150px" style="padding: 0 20px 20px 0" |[[Image:Gm1.png|155px]] Screenshot of [[grid_mode|Grid Mode]] in action.
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<DynamicPageList>
|valign="top"|
imagecontainer=Covers
{|style="background-color: transparent;" width="100%"
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! style="font-weight: bold; font-size: 110%; text-decoration: underline; color: #000; padding: 12px; text-align: left;" | Scripts &amp; Plugins
escapelinks=false
|-
openreferences=true
| style="padding: 3px 5px 10px 15px;"| &diams; [[Colorama]] --a PyMOL plugin which allows to color objects using adjustable scale bars
listseparators=[[,%PAGE%,|thumb|185px|A Random PyMOL-generated Cover.  See [[Covers]].]],\n
|-
ordermethod=none
| style="padding: 3px 5px 10px 15px;"| &diams; [http://ase-web.rit.edu/~ez-viz/ProMOL_dl.html ProMOL] plugin added.  Catalytic site prediction, other tools.  Redirects to website.
allowcachedresults=false
|-
</DynamicPageList>
| style="padding: 3px 5px 10px 15px;"| &diams; [[EMovie]] plugin added.  Easy movies in PyMol using a GUI.
 
|-
| style="padding: 3px 5px 10px 15px;"| &diams; [[DYNMAP]] plugin page created.  Check it out!
|-
| style="padding: 3px 5px 10px 15px;"| &diams; [[EZ-Viz]]
|}
|width="150px" style="padding: 0 20px 20px 0; text-align:left" |[[Image:COLORAMA-screenshot.jpg|125px]] Screenshot of [[Colorama]].
|}
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Latest revision as of 11:54, 12 March 2024

hosted by SBGridlogo2.jpg
Welcome to the PyMOL Wiki!
The community-run support site for the PyMOL molecular viewer.
To request a new account, email SBGrid at: accounts (@) sbgrid dot org
Quick Links
Tutorials Table of Contents Commands
Script Library Plugins FAQ
Gallery | Covers PyMOL Cheat Sheet (PDF) Getting Help
News & Updates
Official Release PyMOL v3.0 has been released on March 12, 2024.
New Plugin CavitOmiX calculate Catalophore™ cavities, predict protein structures with OpenFold by NVIDIA-BioNeMo, ESMFold and retrieve Alphafold models
Official Release PyMOL v2.5 has been released on May 10, 2021.
Python 3 New Python 3 compatibility guide for scripts and plugins
POSF New PyMOL fellowship announced for 2022-2023
Tutorial Plugins Tutorial updated for PyQt5
New Plugin PICv is a new plugin for clustering protein-protein interactions and visualization with available data from PDBe
Selection keywords New polymer.protein and polymer.nucleic selection keywords. Thanks everyone who participated in the poll!
Plugin Update MOLE 2.5 is an updated version of channel analysis software in PyMOL
New Script dssr_block is a wrapper for DSSR (3dna) and creates block-shaped nucleic acid cartoons
Older News See Older News.
Did you know...

Lines

Lines is name of the basic representation for atoms and bonds in PyMOL. Lines is a very simple representation, where each atom bond is displayed as a single colored line, and each atom is displayed as the intersection of any two or more non-terminal bonds.

Usage

# show everything as lines
show lines

# only show residues 50-80 as lines
show lines, i.50-80

Examples

Example: Displaying dashed lines between two atoms

The following commands will create a dashed line between two atoms. 

# first, create two named selections
select a, ///A/501/02
select b, ///B/229/N
# calculate & show the distance from selection a to selection b.
distance d, a, b
# hide just the distance labels; the 
# dashed bars should still be shown
hide labels, d

Technically, the object d is a labelled distance, only the label is hidden. When ray-tracing the image, the dashes come out a bit fat. You can slim them with <source lang="python"> set dash_gap, 0.5 set ..→

A Random PyMOL-generated Cover. See Covers.


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